New file with protein and protein-ligand interaction is added.

[karolamik13]

I created new module which compute protein and protein-ligand interactions.
For protein-ligand interactions there are some additional requirements i.e. installation of Openbabel and PLIP.
There is also new function which after Openbabel installation can provide adding hydrogens to protein and ligand structures.

[jamesmkrieger]

It could be good to provide an option for adding hydrogens using PDBFixer too.

[karolamik13]

Thank you James. Best, Karolina pon., 1 lut 2021 o 13:24 James Krieger <notifications@github.com> napisał(a):

…

***@***.**** commented on this pull request. ------------------------------ In prody/proteins/interactions.py <#1292 (comment)>: > + a1, b1, c1, a2, b2, c2 = calcPlane(sele1)[:3]+calcPlane(sele2)[:3] + RingRing_angle = calcAngleBetweenPlanes(a1, b1, c1, a2, b2, c2) # plane is computed based on 3 points of rings + RingRing_distance = calcDistance(calcCenter(sele1.getCoords()),calcCenter(sele2.getCoords())) + if RingRing_distance < distA and angle_min < RingRing_angle < angle_max: + PiStack_calculations.append([sele1_name[0]+str(sele1.getResnums()[0]), '_'.join(map(str,sele1.getIndices())), sele1.getChids()[0], + sele2_name[0]+str(sele2.getResnums()[0]), '_'.join(map(str,sele2.getIndices())), sele2.getChids()[0], + round(RingRing_distance,3), round(RingRing_angle,3)]) + + PiStack_calculations = sorted(PiStack_calculations, key=lambda x : x[-2]) + LOGGER.info("Number of detected Pi stacking interactions: {0}.".format(len(PiStack_calculations))) + + return PiStack_calculations + + +def calcPiCation(atoms, distA=5.0, extraSele=None, **kwargs): + """Searching for cation-Pi interaction i.e. between aromatic ring and positively charged residue (ARG and LYS) I don't think searching is the right form of the verb. You could put search as a command or searches as a description. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1292 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEDEMUFGYRFQHMFMRDP224TS42MQ7ANCNFSM4WZNGAXQ> .

[karolamik13]

All except adding PDBFixer is ready.

[jamesmkrieger]

Sounds good

[jamesmkrieger]

Everything looks good except for kwargs for interaction scores

[jamesmkrieger]

A few more minor things

[jamesmkrieger]

The scoring kwargs thing still needs fixing

[jamesmkrieger]

Perhaps you could order it this way round like in the second part of the SHEET header records of the PDB (taken from line 1578 of 2tbv):

O LEU A 263 N VAL A 103

See http://www.wwpdb.org/documentation/file-format-content/format33/sect5.html#SHEET

This would include splitting resnum and resname, which is probably a good idea anyway.